Could you check that your picard-Tools package is correctly patched:
--- a/build.xml +++ b/build.xml @@ -23,7 +23,7 @@ ~ THE SOFTWARE. --> -<project name="picard-public" basedir="." default="all"> +<project name="picard-public" basedir="." default="jar"> <property name="src" value="src/java"/> <property name="src.scripts" value="src/scripts"/> @@ -63,6 +63,9 @@ <fileset dir="${lib}"> <include name="**/*.jar"/> </fileset> + <pathelement path="/usr/share/java/testng.jar"/> + <pathelement path="/usr/share/java/snappy1.0.3-java.jar"/> + <pathelement path="/usr/share/java/jbzip2.jar"/> </path> and that file /usr/share/java/snappy1.0.3-java.jar (symlink to maven-repo) is present with original libsnappy package ? After my tests, everything looks fine on Debian side. Thanks Olivier